"Isn't a Chapter" marks the page as a normal comic page. If you were to click on "Isn't a Chapter" it would change to "Is a Chapter" which would maked the said page a marker, say a cover for the chapter, where it begins. Stuff like that.
(The soap opera webcomic about nothing in particular.)
You could make every single page in your archive a chapter if you wanted, but that would just make things messy. So if, in your archive, you have 30 pages... and those 30 pages are actually two 15-page chapters, you just mark page 1 as a chapter and page 16 as a chapter.
If you enable the homepage then it takes advantage of those settings to make a little table of contents to put on the homepage automatically. Then readers can click on "Chapter 2" and get taken right to page 16.